Fig. 2

Identification of protein-protein interaction (PPI) sub-modules in stage II CRC patients. a The whole PPI network from HPRD database (Release 9) is visualized. Each point represents a protein, and lines for interactions between proteins. b The sub-modules derived from GTOM matrix. The dissimilarity matrix (1-GTOM2) is shown. Proteins (or genes) are ordered by unsupervised hierarchical clustering analysis based on the dissimilarity matrix. Two sub-modules (Module 1 and 4) are magnified. c The GSVA profiles (bottom heat map) of 44 PPI sub-modules in the training dataset. Unsupervised hierarchical clustering analysis is performed for PPI sub-modules (rows, hierarchical tree on the left panel) and patients (columns, hierarchical tree on the upper panel) respectively. The middle panel indicates annotations (clinical or genetic variables) of the patients, with p values estimated by Chi-square test for correlations between these variables and the two clusters. Abbreviations for clinical or genetic variables: F, female; M, male; yrs., years; Adj.Ther., adjuvant chemotherapy; N, no; Y, yes; Mol.Type, the six molecular subtypes defined by the original article; Mut.BRAF, Mut.KRAR and Mut.TP53, somatic mutation status of BRAF/KRAS/TP53; M, mutation; WT, wild type; NA, not available